runMSE: Function to run the TCSAM02 MSE for one harvest strategy

In wStockhausen/rTCSAM02: A set of tools to set up input for, and interact with output from, TCSAM02 model runs

Function to run the TCSAM02 MSE for one harvest strategy

Description

This functions runs the TCSAM02 MSE for one harvest strategy.

Usage

runMSE(
  os = "osx",
  topLevelFolder = ".",
  model = "tcsam02",
  path2model = "",
  HCR = 1,
  numRuns = 3,
  minRunID = 1,
  firstYr = 2018,
  numYrs = 10,
  iSeeds = NULL,
  runBaseModel = TRUE,
  baseModelInfo = list(path = ".", configFile = "ModelConfig.inp", datasets = list(file =
    "Datasets.inp", components = list(Bio = "Info", Fishery = c("TCF", "SCF", "GTF",
    "RKF"), Survey = "NMFS", Growth = "EBS", ChelaHeights = NULL)), pin = TRUE, pinFile =
    "tcsam02.pin", minPhase = 1, jitter = FALSE, iSeed = NULL, calcTAC = TRUE, HCR = 1),
  opModInfo = list(path = ".", configFile = "OpMod.Configuration.inp", optsFile =
    "OpMod.Options.inp", mpiFile = "OpMod.ParametersInfo,inp", pinFile = "opMod.pin",
    minPhase = 5, maxPhase = 6),
  estModInfo = list(path = ".", configFile = "EstMod.Configuration.inp", optsFile =
    "EstMod.Options.inp", minPhase = 5),
  keepFiles = c("tmp.sh", "tcsam02.par"),
  cleanupAll = FALSE,
  test = TRUE,
  verbose = TRUE
)

Arguments

os	'win', 'mac', 'osx', or 'linux'
topLevelFolder	path to top-level folder for MSE model runs
model	TCSAM02 model executable name
path2model	path to model executable
HCR	integer identifying harvest control rule to use
numRuns	number of complete MSE runs to make
minRunID	integer identifying first run label for the series of runs (default=1)
firstYr	first year for projection (i.e., the assessment year, or max year + 1, of base model)
numYrs	number of years to run model forward
iSeeds	matrix (number of total possible runs) x (number of years) of random number seed values (or NULL)
runBaseModel	flag to run base model to calculate TAC and create operating model state for first projection year
baseModelInfo	list of parameters to run base model (if necessary)
opModInfo	list of parameters to run operating model
estModInfo	list of parameters to run estimation model
keepFiles	vector of file names to keep after model run, if cleanupAll is true
cleanupAll	T/F to clean up ALMOST ALL model output files after each run
test	flag (T/F) to run in "test" mode
verbose	flag (T/F) to print diagnostic messages
configFile	path to model configuration file

Details

numRuns is the number of successful iterations the MSE is to complete before stopping. If a model run fails for some reason during an iteration in the MSE, the iteration is restarted from the firstYr with a new seed for the random number generator (RNG). If the input matrix iSeeds is NULL, then the new RNG seed is based on the system clock. However, if the matrix is supplied, the seed is taken from the first element in the "next" row of the matrix (a counter for the total number of MSE iterations is used to track this; a separate counter tracks the number of successful iterations). Thus, if iSeeds is supplied, the number of rows in the matrix needs to be larger than (or equal to) the total number of MSE iterations actually undergone to achieve numRuns successful iterations.

Value

• NULL

wStockhausen/rTCSAM02 documentation built on April 16, 2024, 6:25 a.m.